rs745367693

Variant names:

• chr19-18196042-C-A
• rs745367693
• NM_032683.3:c.608C>A

Your query was ambiguous. Multiple possible variants found:

• chr19-18196042-C-A
• chr19-18196042-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_032683.3(MPV17L2):​c.608C>A​(p.Thr203Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: MPV17L2 NM_032683.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.222

Genes affected

MPV17L2 (HGNC:28177): (MPV17 mitochondrial inner membrane protein like 2) Involved in mitochondrial ribosome assembly and positive regulation of mitochondrial translation. Located in mitochondrial inner membrane. Part of mitochondrial large ribosomal subunit. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.058606327).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MPV17L2	NM_032683.3	c.608C>A	p.Thr203Asn	missense_variant	Exon 5 of 5	ENST00000599612.3	NP_116072.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MPV17L2	ENST00000599612.3	c.608C>A	p.Thr203Asn	missense_variant	Exon 5 of 5	1	NM_032683.3	ENSP00000469836.2
MPV17L2	ENST00000532896.5	n.976C>A		non_coding_transcript_exon_variant	Exon 3 of 3	2
MPV17L2	ENST00000533807.3	n.1035C>A		non_coding_transcript_exon_variant	Exon 4 of 4	2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD3 exomes AF: 0.00000401 AC: 1 AN: 249330 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 135290

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0000556

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.11
BayesDel_addAF	Benign	-0.31	T
BayesDel_noAF	Benign	-0.51
CADD	Benign	8.2
DANN	Benign	0.95
DEOGEN2	Benign	0.00059	T
Eigen	Benign	-0.99
Eigen_PC	Benign	-1.1
FATHMM_MKL	Benign	0.084	N
LIST_S2	Benign	0.39	T
M_CAP	Benign	0.010	T
MetaRNN	Benign	0.059	T
MetaSVM	Benign	-0.61	T
MutationAssessor	Benign	0.69	N
PrimateAI	Uncertain	0.56	T
Sift4G	Benign	0.086	T
Polyphen		0.016	B
Vest4		0.20
MutPred		0.21		Loss of glycosylation at T203 (P = 0.0182);
MVP		0.014
MPC		0.69
ClinPred		0.046	T
GERP RS		-0.38
Varity_R		0.057
gMVP		0.32

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs745367693; hg19: chr19-18306852;